Merge branch 'motor_info_h5' of https://github.com/mspito/pymca into …

…motor_info

.gitignore

@@ -62,6 +62,7 @@ docs/_build/
 # cython generated files
 src/PyMca5/PyMcaGraph/ctools/_ctools/cython/*.c
 src/PyMca5/PyMcaPhysics/xas/_xas/cython/*.c
+src/PyMca5/PyMcaMath/mva/_cython_kmeans/*.c
 
 # PyCharm meta data
 .idea/

src/PyMca5/PyMcaCore/NexusTools.py

@@ -510,6 +510,55 @@ def getPositionersGroup(h5file, path):
                 positioners = group
     return positioners
 
+def getStartingPositionersGroup(h5file, path):
+    """
+    Retrieve the start positioners group associated to a path
+    retrieving them from the same entry.
+
+    It assumes they are either in:
+
+    - NXentry/NXinstrument/positioners_start or 
+    - NXentry/NXinstrument/positioners or
+    - NXentry/measurement/pre_scan_snapshot
+
+    """
+    entry_path = getEntryName(path, h5file=h5file)
+    instrument = getNXClassGroups(h5file, entry_path, ["NXinstrument", b"NXinstrument"], single=True)
+    positioners = None
+    if len(instrument):
+        instrument = instrument[0]
+        for key in instrument.keys():
+            if key in ["positioners_start", b"positioners_start"]:
+                positioners = instrument[key]
+                if not isGroup(positioners):
+                    positioners = None
+    if positioners is None:
+        positioners = getPositionersGroup(h5file, path)
+    return positioners
+
+def getStartingPositionerValues(h5file, path):
+    """
+    Retrieve the start positioners names, values and units associated to a path
+    retrieving them from the same entry.
+
+    It assumes they are either in:
+
+    - NXentry/NXinstrument/positioners_start or 
+    - NXentry/NXinstrument/positioners or
+    - NXentry/measurement/pre_scan_snapshot
+
+    """
+    nxpositioners = getStartingPositionersGroup(h5file, path)
+    positions = list()
+    if nxpositioners is None:
+        return positions
+    for name, dset in nxpositioners.items():
+        if not isinstance(dset, h5py.Dataset):
+            continue
+        idx = (0,) * dset.ndim
+        positions.append((name, dset[idx], dset.attrs.get("units", "")))
+    return positions
+
 def getMeasurementGroup(h5file, path):
     """
     Retrieve the measurement group associated to a path

src/PyMca5/PyMcaGui/io/hdf5/NexusInfo.py

@@ -0,0 +1,101 @@
+import h5py
+
+from PyMca5.PyMcaGui import PyMcaQt as qt
+from PyMca5.PyMcaCore.NexusTools import getStartingPositionerValues
+
+from . import HDF5Info
+
+
+class NexusMotorInfoWidget(qt.QWidget):
+    def __init__(self, parent):
+        super().__init__(parent)
+
+        self.mainLayout = qt.QVBoxLayout(self)
+        self.mainLayout.setContentsMargins(0, 0, 0, 0)
+        self.mainLayout.setSpacing(2)
+
+        self.label = qt.QLabel(self)
+        self.label.setText("Number of motors: 0")
+
+        column_names = ["Name", "Value", "Units"]
+        self._column_names = column_names
+
+        self.table = qt.QTableWidget(self)
+        self.table.setColumnCount(len(column_names))
+        for i in range(len(column_names)):
+            item = self.table.horizontalHeaderItem(i)
+            if item is None:
+                item = qt.QTableWidgetItem(column_names[i], qt.QTableWidgetItem.Type)
+            item.setText(column_names[i])
+            self.table.setHorizontalHeaderItem(i, item)
+        self.table.setSortingEnabled(True)
+
+        self.mainLayout.addWidget(self.label)
+        self.mainLayout.addWidget(self.table)
+
+    def setInfoDict(self, ddict):
+        if "motors" in ddict:
+            self._setInfoDict(ddict["motors"])
+        else:
+            self._setInfoDict(ddict)
+
+    def _setInfoDict(self, ddict):
+        nrows = len(ddict.get(self._column_names[0], []))
+        self.label.setText("Number of motors: %d" % nrows)
+        self.table.setRowCount(nrows)
+
+        if not nrows:
+            self.hide()
+            return
+
+        for row in range(nrows):
+            for col, label in enumerate(self._column_names):
+                text = str(ddict[label][row])
+                item = self.table.item(row, col)
+                if item is None:
+                    item = qt.QTableWidgetItem(text, qt.QTableWidgetItem.Type)
+                    item.setFlags(qt.Qt.ItemIsSelectable | qt.Qt.ItemIsEnabled)
+                    self.table.setItem(row, col, item)
+                else:
+                    item.setText(text)
+
+        for col in range(len(self._column_names)):
+            self.table.resizeColumnToContents(col)
+
+
+class NexusInfoWidget(HDF5Info.HDF5InfoWidget):
+
+    def _build(self):
+        super()._build()
+        self.motorInfoWidget = NexusMotorInfoWidget(self)
+        self.addTab(self.motorInfoWidget, "Motors")
+
+    def setInfoDict(self, ddict):
+        super().setInfoDict(ddict)
+        self.motorInfoWidget.setInfoDict(ddict)
+
+
+def getInfo(hdf5File, node):
+    """
+    hdf5File is and HDF5 file-like insance
+    node is the posix path to the node
+    """
+    info = HDF5Info.getInfo(hdf5File, node)
+    info["motors"] = get_motor_positions(hdf5File, node)
+    return info
+
+
+def get_motor_positions(hdf5File, node):
+    node = hdf5File[node]
+
+    nxentry_name = node.name.split("/")[1]
+    if not nxentry_name:
+        return dict()
+
+    nxentry = hdf5File[nxentry_name]
+    if not isinstance(nxentry, h5py.Group):
+        return dict()
+
+    positions = getStartingPositionerValues(hdf5File, nxentry_name)
+    column_names = "Name", "Value", "Units"
+    return dict(zip(column_names, zip(*positions)))

src/PyMca5/PyMcaGui/io/hdf5/QNexusWidget.py

@@ -47,7 +47,7 @@
     QString = str
 
 from . import HDF5Widget
-from . import HDF5Info
+from . import NexusInfo
 from . import HDF5CounterTable
 from . import HDF5McaTable
 from . import QNexusWidgetActions
@@ -123,7 +123,7 @@ def __init__(self, parent=None, mca=False, buttons=False):
         self._autoCntList = []
         self._autoAliasList = []
         self._defaultModel = HDF5Widget.FileModel()
-        self.getInfo = HDF5Info.getInfo
+        self.getInfo = NexusInfo.getInfo
         self._modelDict = {}
         self._widgetDict = {}
         self._lastWidgetId = None
@@ -507,8 +507,9 @@ def showInfoWidget(self, filename, name, dset=False):
             phynxFile  = self.data._sourceObjectList[fileIndex]
         else:
             phynxFile  = HDF5Widget.h5open(filename)
+
         info = self.getInfo(phynxFile, name)
-        widget = HDF5Info.HDF5InfoWidget()
+        widget = NexusInfo.NexusInfoWidget()
         widget.notifyCloseEventToWidget(self)
         title = os.path.basename(filename)
         title += " %s" % name
@@ -531,6 +532,7 @@ def sourceObjectDestroyed(weakrefReference):
                     del self._widgetDict[wid]
             widget._sourceObjectWeakReference = weakref.ref(phynxFile,
                                                  sourceObjectDestroyed)
+
         widget.setInfoDict(info)
         # todo: this first `if` block can be dropped when silx is a hard dependency
         if dset and Hdf5NodeView is None: